I have a D44/D60 in my ZJ and thus have abandoned the ABS. My plan is to eventually gut it completely and redo the lines as needed. Problem is that on my '93 to properly bleed the brakes after running the master dry is I have to cycle the ABS module/pump.
Fortuantly I have a scan tool at work to do this. Unfortunatly all the sensors have to be hooked up to do it. So if I mess with the master cylinder or have the lines open for an extended time to do an axle swap and the master runs dry, I have to dig out all the ABS sensors(fortunatly I kept them), hook them up and then cycle the system.
Other than that I have had no issues with having the ABS system still in.
I have read as well that there are some goofy metric lines in the mix that can cause problems with hooking the lines directly to the master.
This is on a '93 ZJ and you may not encounter these problems.